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Crystal Structure of E. coli polynucleotide phosphorylase bound to RNA and RNase E
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E3H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293.15 0.2 M ammonium hydrogen citrate, 17 % w/v PEG 3350, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 3.84 67.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 176.335 α = 90 b = 176.335 β = 90 c = 189.628 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD MARMOSAIC 225 mm CCD Monochromator 2006-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.5 20 99.3 6.6 102846 97645 2 2 27.176
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.59 99.5 0.619 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1E3H 2.5 20 102846 97645 5134 99.36 0.201 0.16911 0.16639 0.2005 0.22065 0.2279 RANDOM 27.176
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.495 r_dihedral_angle_4_deg 20.703 r_dihedral_angle_3_deg 15.951 r_dihedral_angle_1_deg 6.735 r_scangle_it 5.44 r_scbond_it 3.361 r_mcangle_it 2.01 r_angle_refined_deg 1.939 r_angle_other_deg 1.247 r_mcbond_it 1.229
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.495 r_dihedral_angle_4_deg 20.703 r_dihedral_angle_3_deg 15.951 r_dihedral_angle_1_deg 6.735 r_scangle_it 5.44 r_scbond_it 3.361 r_mcangle_it 2.01 r_angle_refined_deg 1.939 r_angle_other_deg 1.247 r_mcbond_it 1.229 r_nbtor_refined 0.309 r_nbd_refined 0.228 r_symmetry_vdw_refined 0.193 r_xyhbond_nbd_refined 0.161 r_symmetry_hbond_refined 0.159 r_chiral_restr 0.152 r_nbd_other 0.14 r_nbtor_other 0.051 r_bond_refined_d 0.022 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12865 Nucleic Acid Atoms Solvent Atoms 884 Heterogen Atoms 167
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling